Arsenic is found naturally in the Earth’s crust. Changes in agricultural processes in rural areas (increased fertilization) causes bacteria to release arsenic from the soil into the groundwater, from whence it finds its way into the drinking water of an estimated 137 million people in 70 countries. At levels as low as 10 ppb (that’s ten parts arsenic per billion parts water), people begin to suffer from a myriad of severe illnesses and may even die. There are ways to remove arsenic, but they tend to be expensive and to produce toxic sludge that must then be dealt with.

Enter SAR, which relies on oxidation and filtration, uses no chemicals and produces no sludge. Simply by aerating the groundwater in an SAR plant, arsenic, iron and manganese are precipitated back into the soil deep underground. The cost of a single plant capable of cleaning 6000 liters of water per day is only about $4000.

After using SAR in rural Bellingham, Northwest Washington State, arsenic levels fell to below the safe limit set by the US Environmental Protection Agency. There are plans to set up new SAR plants in Cambodia, Vietnam and Mexico.

Wednesday, March 30, 2011

Did you know there are about seventeen quadrillion flies on Earth?Neither did I.Apparently, there are some 200,000 species of true fly (insects with a single pair of wings, order Diptera).Thanks to the work of Brian Wiegmann of North Carolina State University and a large international team of entomologists and geneticists, we have a better picture of how all these flies are related to each other.

Flies have been around for 260 million years.Among other adaptations, during that time, twelve different groups of flies have taken to feeding on blood, and eighteen types of flies have lost their wings.They’ve evolved the ability to live in an amazing variety of places, either as adults or as larvae.According to Wiegmann:

There are fly larvae that live in petroleum, in hot springs, in the gills of land crabs, on the dung of millipedes and within bee hives.

The researchers compared the mitochondrial and nuclear DNA of an assortment of flies to assemble an evolutionary tree for these flies.Many of the results were expected. Flies that had been grouped together by physical traits turned out to be genetically related as well.However, there was at least one major surprise.The fruit fly Drosophila, which may be the most common animal model in all of science, turned out to be most closely related to a couple of insect parasites, including a wingless fly that lives on honeybees.Who could have seen that coming?

Thanks to the painstaking work of collecting fly samples and sequencing their DNA, we now have an understanding of how flies evolved.This in turn, gives us a better understanding of evolution in general, always a plus.

Tuesday, March 29, 2011

Howard Friedman and Leslie Martin from the University of California, Riverside have been studying the factors that allow people to live long lives. The Longevity Project: Surprising Discoveries for Health and Long Life from the Landmark Eight-Decade Study is the result of their two decade long project.

Much of the data was first gathered by the late Louis Terman of Stanford University, who studied 1500 ten-year-old children, starting in 1921. Those children were followed over the decades, and extensive notes were taken on every aspect of their lives. When Friedman and Martin took over the project in 1991, they enlisted the help of graduate and undergraduate students to track down additional information about the Terman participants.

The results were somewhat startling. In particular, the researchers did not expect to see that the most cheerful, optimistic, happy kids had not lived as long as their more serious counterparts. Also, persistent hard-working people lived longer than more relaxed stress-free people.

You may or may not be surprised by some of the other findings:

Men in long-term marriages lived the longest, followed by those who never married, and trailed by those who had been divorced. Women’s longevity was not greatly affected by marriage or divorce.

Pets do not extend life expectancy, nor does feeling loved. On the other hand, helping others and participating in health-promoting groups does extend life expectancy.

Here’s one that really surprised me. According to the authors, starting formal education too early (first grade before age 6) is linked to earlier mortality.

Personally, I think this study was a bit small to make these kinds of sweeping statements. It does give one pause though. You can see Friedman and Martin discuss their project here:

Monday, March 28, 2011

Many parents sleep soundly knowing that their home smoke detectors will awaken them and their children in case of a fire.Unfortunately, that doesn’t seem to hold true for children.Dorothy Brock and Ian Thomas of Victoria University, Melbourne conducted a small study testing whether children will wake up to alarms.The chilling answer is that most will not.

The parents of 123 children aged 5 to 15 were asked to wait until the kids had been asleep for at least an hour and then set off the nearest smoke detector for 30 seconds.The parents then charted whether the kids woke up at all, and if they did, whether they understood why they had been awakened and what they should do (i.e. evacuate the house).Overall, 78% of the children slept right through the alarm.In the 5 to 10 age group, a whopping 87% slept through.Of the lighter sleepers who did wake up, less than half indicated that they knew they must leave the house.

If this data holds true, only about 10% of kids can be relied upon to respond to a smoke alarm by waking up and leaving the house.In this study, the alarms were only sounded for 30 seconds.In all likelihood, an ongoing claxon would eventually awaken more children.However, in a fire, those extra minutes can be extremely costly.

According to Bruck:

Parents should not rely on their children waking to the smoke alarm in the event of a fire and should not assume that they will immediately evacuate if they do wake up to a fire.

Sunday, March 27, 2011

Just as laparoscopy revolutionized surgery a few decades ago, now a new technique undergoing clinical trials is setting the stage for the surgery of the future. Natural Orifice Translumenal Endoscopic Surgery (NOTES) may very well be the wave of the future.

Unlike traditional surgeries, NOTES does not require any external incisions. Instead, as the name implies, surgeons make use of natural orifices, most often the mouth or vagina. Surgical instruments are threaded into the body and then internal incisions through either the vaginal wall or digestive tract place the implements where they are needed. Because the affected internal areas have few pain receptors, in sharp contrast to skin, patients require far less pain medication either during or after the procedures.

Thus far, doctors have successfully removed gall bladders, kidneys and appendixes, and repaired hernias via this method. The easiest orifice to use seems to be the vagina, which gives women an obvious advantage. However, the Natural Orifice Surgery Consortium for Assessment and Research (NOSCAR), formed in 2006, is conducting clinical trials in the hopes of bringing scarless surgery to everyone.

Saturday, March 26, 2011

Light pollution has always been the bane of stargazers. A new study by Christopher Kbya and his team from the Institute for Space Sciences and the Leibniz-Institute shows just how pervasive this problem has become. According to them, on a cloudy day in Berlin the sky is ten times brighter than it would be without the anthropomorphic light sources.

Berlin at night

Photo: C Kyba.

Historically, astronomers have only measured the amount of light pollution on cloudless nights since they don’t tend to use their light telescopes on cloudy nights. And light pollution is a problem even on clear nights. However, as clouds serve to redirect light back in the direction from whence it came, the problem can be magnified many times on cloudy nights. This isn’t so much a problem for astronomers, again, they aren’t looking at the sky on cloudy nights anyway. It could be a huge problem for the plants and animals that rely on the absence of light to trigger their reproductive and behavioral cycles.

I should add that all the light measurements were taken on moonless nights, and yet the amount of light in the urban settings was comparable to that of a full moon in a rural setting. Many organisms have not only day/night cycles but also monthly rhythms that depend on the lunar stages, especially the times of full or new moons. Although the authors did not test this directly, it’s easy to assume that such creatures would be seriously disoriented by the light pollution coming from our cities.

If you want to help astronomers assess the amount of light pollution in your area, you can participate in the Globe at Night project. Phil Plait has more information about this on his Bad Astronomy blog.

Sepsis, also called blood poisoning, can result from an unchecked infection that spreads through the bloodstream. The body reacts to this threat by undergoing a systemic inflammatory response.In up to half of all cases, the eventual prognosis is organ failure and death.There is a clear need for better treatments.

Enter the humble roundworm, Acanthocheilonema viteae, actually a parasitic nematode.These tiny creatures, barely visible to the naked eye, infect as many as a quarter of the world’s population.They also secrete a protein called ES-62 that is known to suppress inflammation. The ES-62 protein induces a process of autophagy (‘self-eating’) in which damaged cells and tissues are cleared from the body, preventing systemic inflammation and leaving healthy tissue.

This property is sometimes exploited by people suffering from allergies or autoimmune diseases, who willingly infect themselves with the little worms.Happily, the researchers, led by Alirio Melendez of the National University of Singapore, have found that the protein alone works just as well. The scientists induced sepsis in mice, and then successfully protected those mice from septic shock by administering ES-62.

Melendez anticipates using this protein to treat humans as well:

The findings suggest that ES-62 could be used to induce autophagy and reduce the overwhelming inflammation that is responsible for the massive tissue damage seen in sepsis.

Wednesday, March 23, 2011

Zengbo Wang from the University of Manchester and his colleagues from that university and from the University of Singapore have extended the range of optical microscopes by at least twenty fold. To do so, they make use of transparent structures called microspheres, creating what they call a ‘microsphere nanoscope’.

Traditional optical microscopes cannot be used to discriminate objects less than one micrometer (a thousandth of a millimeter) apart. By adding the microspheres, that limit has been dropped to 50 nanometers (millionths of a millimeter). The ability of the tiny spheres to amplify images is theoretically limitless, possibly allowing researchers to watch viruses (which are typically measured in nanometers) in action.

Schematic of the transmission mode microsphere superlens integrated with a classical optical microscope. The spheres collect the near-field object information and form virtual images that can be captured by the conventional lens.

Tuesday, March 22, 2011

The South American rainforests contain fungi that enslave and kill ants. Thanks to the work of Harry Evans and Simon Elliot of Federal University of Viçosa, and of David Hughes from Penn State University, we can add four new species of parasitic fungi to the pantheon.

These four new subspecies of fungi, which fall within the genus Ophiocordyceps, prey on different species of carpenter ant. In each case, upon infection the fungus takes over the ant’s brain, forcing the ant to attach itself to a suitable location for spore dispersal. It is the manipulation of the ant’s behavior that earns these fungi the name ‘Zombie ant fungus’. After the ant is placed to the fungus’ satisfaction, one or more fruiting bodies grow out of the ant’s head. These stalks serve to disperse new spores that can continue the fungi’s life cycle.

And now we have four more kinds of these little parasites. Here’s some footage of this kind of fungi narrated by David Attenborough, though if you’re squeamish, you may not wish to watch.

Almost 3000 healthy volunteers over the age of 13 who ran at least ten miles/week were divided into stretching and non-stretching groups.For three months, the runners in the stretching group followed a prescribed 3 to 5 minute stretching routine before each run.The runners in the non-stretching group did not stretch at all but simply started running.Any injury that prevented running for at least a week was recorded by self-evaluation.

About half the initial participants (1,398) completed the three-month regiment.These were divided into 600 stretchers and 798 non-stretchers.The injury rate was identical in both groups, at 16% of runners.In other words, for most people, stretching neither prevents nor causes injury.

In fact, the leading causes of running-related injuries are having had an injury within the previous four months and having a high body mass index.However, there was one subset of people for whom not stretching was problematic:the runners in the not-stretching group who normally did stretch.Those who changed their pre-run regiment from stretching to not stretching increased their injury rate by 40%.

What I get out of this is that if you are a runner and haven’t been stretching before each run, don’t start now.As a friend of mine once pointed out, it’s not as if our ancestors did a few calisthenics before chasing down that antelope.On the other hand, if you have been stretching, you’d better keep it up.

Sunday, March 20, 2011

Lijun Yin of Binghamton University is attempting to make computers understand facial expressions. Although, this might make computers easier for everyone to use, he especially sees a need for this technology among those who have a limited ability to communicate.

Earlier, Yin collaborated with Peter Gerhardstein, also from Binghamton University, to create a 3D facial expression library. That database, made from 2500 facial expressions of 100 different people, is available for free to nonprofit research groups. Since then, Yin has been attempting to teach computers to read those same emotional cues. The challenge is to translate tiny changes around a subject’s eyes or mouth into a language that computers can interpret.

As Yin says:

Computers only understand zeroes and ones. Everything is about patterns. We want to find out how to recognize each emotion using only the most important features.

If successful, Yin anticipates a myriad uses for the new technology, from determining whether patients are in pain to detecting lies. Perhaps one day, our computers will read our moods and start us off with some soothing music before they display our credit card bills.

Saturday, March 19, 2011

How come my daughter picks up the newest tae kwan do moves in a matter of minutes, and I’m still struggling with them months later?According to Charlotte Stagg and her team from the University of Oxford, the answer may lie in our responsiveness to GABA.

GABA (gamma-Aminobutyric acid), pictured above, is a neurotransmitter.Although structurally an amino acid, it is not incorporated into proteins but instead acts to regulate neural activity and muscle tone.Stagg and her colleagues wondered whether differences in responsiveness to GABA might affect motor learning as well.

To that end, the scientists measured GABA levels in volunteers both before and after those levels were decreased artificially by anodal transcranial direct current stimulation (low level current applied to their scalps).These magnetic resonance spectroscopy scans gave the researchers information about baseline GABA levels and GABA responsiveness in the participants. On a different day, the same volunteers were again scanned for GABA levels, this time while attempting to memorize and execute a sequence of finger motions.Those who had been more responsive to GABA learned the motions more quickly.

The scientists hypothesize that GABA responsiveness may affect one’s ability to make the neural connections necessary for learning and memory.In that case, controlling GABA levels may result in a potential treatment for brain trauma.

Friday, March 18, 2011

On March 19th, we'll be treated (weather permitting) to a view of the largest full moon since 1993. The Moon's orbit around the Earth is slightly elliptical, rather than circular, meaning that at some times the Moon is closer to the Earth than at others. The closest approaches (at perigee) make the moon appear 14% larger than at its farthest (apogee).

When Loucks and his colleagues looked at people of similar age, completing graduate school compared with not finishing high school gave women a 2.86 mmHg advantage and men a 1.25mmHg advantage.Next, the researchers examined the records of individuals who had all started with the same blood pressure thirty years ago, and checked to see how their blood pressure changed over time.Women who went on to complete graduate school during the intervening thirty years had 2.53 mmHg lower blood pressure than those who hadn’t finished high school.For men, the advantage was only 0.34 mmHg.

These differences are far too small to spell the difference between health and cardiovascular illness by themselves.However, it is also known that people with more than seventeen years of education tend to have a lower body mass index, and to smoke and drank less than people with less than twelve years of education.What I wonder is whether a person could get a similar benefit from a lifetime of independent curiosity and learning.

The flora and fauna in remote forests and jungles has been a rich source of medicines and other products. However, the ecosystems and political systems of those regions can be adversely affected by collection attempts. To prevent ‘biopiracy’ (stealing valuable biological resources without compensating the local people) or habitat destruction, the Convention on Biodiversity went into affect in 1993. That United Nations treaty declared that nations hold rights to their own biological materials.

Last fall, the Nagoya protocol was drafted. For one thing, it clarifies procedures for getting collection permits. In the past, it wasn’t clear whether researchers on a collecting mission should approach the local university or the town hall. Nagoya requires that there be one national access point to field those requests. The treaty also requires collectors to respect indigenous people’s laws and customs, and spells out how local communities should be compensated for such collections.

The new protocols are expected to be helpful to researchers who know exactly what they are looking for. The procedure for obtaining permission to collect a specific type of seed or fungus, for example, has been streamlined. However, some scientists fear that Nagoya will make early-stage exploratory expeditions, where many kinds of specimens are collected (most of which will prove to be worthless), more complicated.

Tuesday, March 15, 2011

You may recall that the Mars500 project, a joint venture of the European Space Agency (ESA) and the Russian Institute of Biomedical Problems (IBMP), is underway. This 520-day simulation of a trip to Mars involves six volunteers sealed in an isolation chamber in Moscow. The crew has successfully completed the simulated trip to Mars and the thirty-day stay on that planet, and is now pretending to be flying home.

At the beginning of the mission, crewmember Diego Urbina provided this video tour:

Besides coping with isolation and cramped quarters for a year and a half, the crew of a real mission to Mars must also be ready to handle all kinds of emergencies, from equipment failure to medical crises. Not only could such a crew not expect any physical aid from Earth (no rescue would be possible) but they may not even have the luxury of waiting for technical support. Depending on where the spacecraft is, it can take up to forty minutes to ask a question and receive an answer from Earth. Self-sufficiency is essential.

To that end, the Mars500 crew underwent emergency medical training, including procedures that have been modified to work without gravity. During the flight, they’ve been given medical tasks to perform on a doll as well as a series of other experiments and tasks. Thus far, everything is going well.

Monday, March 14, 2011

The p53 gene, named for the size of its protein (53 kilodaltons), is the most frequently mutated gene in human cancers.Normally, p53 functions as a ‘tumor suppressor’ regulating other genes involved in growth.Researchers from the University of Pennsylvania and the University of Science and Technology of China have discovered that p53 also plays an important role in glucose metabolism.

Glucose can be stored as a sugar, turned into energy, or used in the production of nucleic acids and lipids.The first enzyme in the glucose metabolism pathway is called glucose-6-phosphate dehydrogenase (G6PD).G6PD is also the rate-limiting step of the entire pathway, meaning that the speed of glucose turnover depends largely on the amount of available G6PD.

The researchers found that wild-type (normal) p53 proteins bind to and inactivate G6PD.This in turn limits the amount of glucose that the cell can take up.Mutant p53 does not bind to G6PD.This goes a long way to explaining why tumor cells, which are very often p53 mutants, tend to take up glucose so much more quickly than healthy cells, something that has long puzzled oncologists.

Even more intriguing, p53 appears to function as an enzyme itself.After binding to p53, G6PD is converted to an inactive form and remains in that form even after p53 releases it.In other words, p53 has catalyzed a change in G6PD.You only need 3% as much p53 as G6PD in a cell to dampen the glucose metabolism pathway, but without functional p53, the cells can process glucose with abandon.

Sunday, March 13, 2011

First, the volunteers were seated at a table with a realistic looking right arm carefully positioned next to their real right arm. The experimenter then stroked and touched both right arms (real and rubber) in an identical manner. You can see this part of the experiment in the picture below. This stimulation caused the subjects to experience both right arms as belonging to their own bodies.

The next part of the experiment makes me wonder whether the volunteers knew what they were in for. To test how completely the subjects associated the rubber arms with their own bodies, the scientists proceeded to threaten each arm with a kitchen knife. This somewhat bizarre methodology was accompanied by physiological stress tests. The volunteers were just as freaked out by the thought of the experimenters stabbing their fake hands as their real ones, indicating that they really did feel like they possessed three biological arms.

The scientists see two future benefits to tricking the brain in this manner. We could offer stroke or amputee patients synthetic arms that would feel just like the ones they lost. We could also provide extra arms for people who are too busy to manage with just the two.

The researchers removed 15% of the heart tissue from newborn mice. To their surprise, the infant mice were able to regrow the tissue. The resultant hearts looked and performed exactly like normal hearts. This ability was retained until the mice were seven days old, at which point they lost the capacity to grow new heart muscle. To put that in perspective, mice reach maturity between 6 to 8 weeks and can live for two or three years. Thus, the ability to fix heart problems continues for a large part of the mouse’s ‘childhood’.

The scientists believe that the infant mice’s cardiomyocytes, the beating cells of the heart, can stop beating and divide, repairing the damage. The next step is to figure out whether adult heart cells could be reprogrammed in the same manner. If so, there may be a way to induce human cardiomyocytes to repair heart defects.

Thursday, March 10, 2011

The ability to follow the direction of a gaze even around a barrier is a key tool in nonverbal communication between individuals. Previously, this ability had only been observed in birds and primates. Friederike Range and Zsófia Virányi of the University of Vienna have now detected this behavior in captive wolves.

There are two key components to the gaze test. The first is to see whether the test subject will follow a gaze into the distance. In other words, will the animal look in the same direction as the tester is looking? If so, then the animal understands that there may be something important going on where the tester is looking. Many types of animals, including wolves, birds and even a tortoise can pass this test.

Gaze following into distant space.

A: control trial; B: test trial.

doi:10.1371/journal.pone.0016888.g004

The second, more complex test is to see whether the animal will follow a gaze around a barrier. If the tester appears to be looking at something that is blocked from the animal’s view, will the animal shift its position to investigate? Far fewer animals can make this cognitive leap, but wolves happen to be one of them. However, when the wolves repeatedly found nothing of interest behind the barrier, they stopped paying attention to the testers’ gazes in that direction. In contrast, they did not habituate to stares into the distance, but continued to look in the direction their handlers were looking. This may indicate that following a gaze around a barrier requires a different cognitive process than simply following a gaze into the distance.

Layout of the barrier test, showing the position of the human E 1 and the start position of the test subject.

E2 held the subject on the collar or leash until the gaze cue was given. The arrows indicate where E 1 looked in the test and control conditions respectively.

doi:10.1371/journal.pone.0016888.g001

I don’t know about you, but I can’t wait to try this experiment out on my dog. I find the fact that the researchers used dogs as well as humans to indicate gaze directions to the wolves particularly intriguing.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.